EVOLUTION OF Fusarium TAXONOMY
Transcript of EVOLUTION OF Fusarium TAXONOMY
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EVOLUTION OF Fusarium TAXONOMY: MORPHOLOGICAL, BIOLOGICALAND PHYLOGENETIC DIAGNOSTIC CONCEPTS
EVOLUTION OF Fusarium TAXONOMY: MORPHOLOGICAL, BIOLOGICALAND PHYLOGENETIC DIAGNOSTIC CONCEPTS
Luis Pérez Vicente
OMNIPRESENT IN SOIL, WATER, AIR AND OTHER MULTIPLE
SUBSTRATES; ARE SAPROPHYTES, PATHOGENS,
ANTAGONISTS
Fusarium species as plant pathogens
Fusarium species are human, animal and plant pathogens
Fusarium spp. cause diseases in a wide range of host plants. At least 81 of 101 economically important crop plants of APS list of diseases are caused by Fusarium
Some of them have a narrow range of hosts; others have a very wide range as F. oxysporum
They are found in soil, air water and can be transported in vegetable tissues.
They can be recovered from the deepest roots in soil until the higher inflorescences of plants.
Produce toxins and allergies
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Sugarcane wilt by Fusarium sacchari
Pokkah Boeng in sugarcane by Fusarium moniliforme
Diseases caused by different Fusarium species
Stem rot and tubers by Fusarium spp.
Diseases caused by different Fusarium species
Bakanae in rice by F. fujikuroi
Green point gall of cacao by Nectria rigidiuscula(Fusarium decemcellulare)
Flowering malformation of mango by (Fusarium manginifera)
Diseases caused by different Fusarium species
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Oil palm wilt by F. oxysporum f. sp. elaeidis
F. oxysporum f. sp. lycopersici
Diseases caused by different Fusarium species
Panama disease by F. oxysporum f. sp. cubensis
Crown rot by F. pallidoroseum
Diseases caused by different Fusarium species
Gibberella zeae(F. graminearum) Papaya internal fruit rot by
Fusarium spp.
Diseases caused by different Fusarium species
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Fusarium taxonomy
The taxonomy of Fusarium genus has been affected by species concept changes
In this process in the last 100 years have been recognized by taxonomist, as few as 9 and as much as 1000 species.
1809. Link create genus Fusarium
1910. Appel and Wollenweber (1910) grouped all imperfect fungi Tuberculariacea that have pluricelular macroconidia with croissant shape developed on sporodochia.
1935. Wollenweber y Reinking publish the monography “Die Fusarien” and split genera in 16 sections and 65 species.
1940. Snyder & Hansen questioned sections described by Wollenweber& Reinking and reduce all variants to 10 species. Beside propose that all the forms of Elegans section belong to a single specie: F. oxysporum
1955. V. I. Bilai publish in URSS “The Fusaria (Biology and Systematics)”
1968. C.M. Messiaen and R. Cassini publish “La systématique des Fusarium”; esencially kept the classification of Snyder & Hansen and propose varieties of some species .
Taxonomy of Fusarium genus:Historic review
1971. C. Booth publish The Genus Fusarium. CMI. (recognize 14 species)
1981. Nelson Tousson y Manasas publish“Fusarium Species: An Illustrated Manual for Identification”.
1982. W. Gerlach y H. Niremberg publih“The genus Fusarium – A pictorial Atlas”. (recognize 21 species)
1980s. The collaboration among taxomomists of EU, Europe. South Africa, and Australia unify criteria of Gerhlach and Niremberg (Germany), Nelson, Tousson y Marasas in (EU) and Burgess et al. (Australia).
1994. L.W. Burgess et al., publish “Laboratory Manual for Fusarium Research”
2006 J. Leslie and B. Summerell publish “ The Fusarium Laboratory Manual” recognize 70 species on base of morphological, biological and phylogenetic criteria.
Taxonomy of Fusarium genus:Historic review
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Relationship among the nine species of Snyder & Hansen, the sections of Wollenweber & Reinking and the species described by Leslie and Summerett (2006)
Species of Sections of Summeret & Leslie Snyder & Hansen Wollenweber (2006)
& Reinking
F. episphaeria Eupionnotes F. dimerum, F. merismoidesMacroconia
F. lateritium Lateritium F. lateritium
F. moniliforme Liseola F. anthophilum, F. circinatum,F. proliferatum, F. subglutinans,F. thapsinum, F. verticillioides,and other species in
Fusarium complex
Gibberella fujikuroi
F. nivale Arachnites No more consider be Fusarium
F. oxysporum Elegans F. oxysporum
F. rigidiuscula Spicarioides F. decemcellulare
Species of Sections of Summeret & Leslie Snyder & Hansen Wollenweber (2006)
& Reinking
F. roseum Discolor F. acuminatum, F. armeniacumGibbosum F. avenaceum, F. compactum; Roseum F. crookwellense, F. culmorum, Arthrosporiella F. equiseti, F. graminearum,
F. longipes, F. heterosporum, F. polyphialidicum, F. pseudograminearum, F. semitectum, F. torulosum
F. solani Martiella F. solaniVentricosum
F. tricinctum Sporotrichiella F. chlamydosporum, F. poae,F. sporotrichioides, F. tricinctum
Relationship among the nine species of Snyder & Hansen, the sections of Wollenweber & Reinking and the species described by Leslie and Summerett (2006)
Fusarium oxysporum Schlecht. ex Fr
F. oxysporum is a complex of anamorphic fungal filamentous species morphologically similars (O’Donnell and Cigelnick, 1998).
F. oxysporum is omnipresent around the world in different soils.
Is the Fusarium taxa more economical and agricultural important (Ploetz, 2006)
Isolations of F. oxysporum are genetically diverse including phytopathogens, saprophytes and biocontrol agents.
They include many plant pathogenic representatives. Cause:
– Vascular wilts,
– Damping-off problems
– Root and stalk base rots
Have been identified 150 formae speciales with unique pathogenicity or to at an important number of close related hosts
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Fusarium oxysporum Schlecht. ex Fr
Wilts are important in many vegetable, fiber, ornamentals palm trees and banana.
Pastures and cereals are not affected by F. oxysporum.
Saprophytic populations usually can be aggressive secondary colonizers of diseased plant parts, particularly roots and are morphologically undistinguished from primary colonizers
Morphology of F. oxysporum colonies are highly variable:
– Produce a floccose sparse or abundant, white to pale violet mycelia.
– Usually produce a pale violet to dark mangenta pigment in agar media ( some isolates do not produce any pigment)
The concepts essentially define criteria to differentiate species. There is three basic concept applied for Fusarium :
Morphologic: (constant observable morphological characters among individuals of the same specie and markedly different between different species).
Biological: (crosses among members of the same specie are sexually fertile with viable and fertile progeny).
Phylogenetic: (ADN sequences of conserved genes are cladistically treated to develop phylogenies of those which are grouped in the same group with a common origin, are considered to be of the same specie)
Species definition concepts
Morphological criteria for specie identification in Fusarium
Morphological characteristics of structures in carnation leaf agar) Macro and microconidia (form, abundance, size, how are
produced (better from a CLA culture) Chlamydospores (present/absent; single, agglomerates) Conidiophores (mono o poliphyalidics)
Cultural characteristics Growth rate (in PDA) Aerial mycelia absent or present and color (PDA) Presence and color of sporodochia in (PDA and CLA) Color of colonies in the superior and inferior part (PDA)
Production of volatile aldehydes (odor; rice grain media)
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Macroconidia cells (Leslie y Summerell, 2006)
Mesoconidiafusoidsfalcates
straight
curved
Basal cells: E) F. culmorum ; F) F. crookwellense; G) F. avenaceum; H) F. culmorum
Apical cells: I) F. culmorum ; J) F. decemcellulare; K) F. avenaceum; L) F. longipes
F. longipes
Microconidia shapes (Summerell et al. 2003)
ovalpyriform
clavatefusiform
napiformglobose
Conidiogenic cells of microconidia phialid.
Microconidia in monophialids
False head
Chains
F. verticilloides
F. solani F. oxysporum
Microconidia in poliphialids
F. clamidosporium
F. semitectum
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Chlamydospores
F. clamidosporum F. oxysporum f. sp. cubense
Morphology of Fusarium oxysporumMycelia floccose sparse or abundant varying from white to purple color.
From pale violet to dark magenta pigment in agar (some isolates do not produce any pigment.
Microconidìa without septa produced in false heads in short monophialides
Can produce pionnotal colonies
Macroconidia developed in ramified conidiophore on sporodochia
Chlamydospores terminal or intercalated; single or in chains
Characteristic of Fusarium growth in CLA
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Morphology of F. oxysporum isolates growth
En CLA and SNA filter paper, produce abundantly microconidia in false heads in short
monophyalids developed in hyphae.
Chlamydospores
Can be observed in hyphae on agar surface or inside media.
Develop on hypha or conidia in old culture of until a month.
True chlamydospores, pseudochlamydospores and swollen cells, can be missed.
– Chlamydospores have a gross verrucose like wall and a light color usually from yellow to brown. Can be presents solitary, in chains aggregates, above or below hypha.
– Pseudochlamydospores (of thin walls, alone or in short chains are present only in F. andiyazi)
– Swollen cells are numerous in Liseola section
A) F. poae; B) F. oxysporum ; C) F. acuminatum; D) F. nelsonii ; E) F. subglutinans; F) F. nygamai; G) F. pseudonygamai; H) F. lateritium; I) F. thapsinum; J) F. decemcellulare; K) F. verticillioides; L) F. culmorum.
Upp
erLo
wer
(Summerett et al., 2003)
Colonies morphology in potato dextrose agar. A considerable variation among Fusarium species
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Biological concept
Fertility of sexual crosses (teliomorphdevelopment)
Host range: formae speciales
Vegetative compatibility groups.
Biologic: fertility of sexual crosses
Most fertility analysis are realized for of Gibberella fujikuroi and Haemanectria haematococca species complex (Fusarium solani) differentiation (Leslie and Summerell 2006).
This approach can not be used to species that do not develop teliomorphe as F. oxysporum.
There are two idiomorphic MAT (MAT-1 and MAT-2) that have to be present for mating occurrence (Kroonstadt and Staben, 1987).
– In F. oxysporum has been reported alleles MAT-1 and MAT-2highly similar to those of fertile Fusarium species
– The not fertility can be consequence of mutation of genes that codify indispensable receptors not codified by MAT locus.
Biologic: fertility of sexual crosses(Protocol described by por Klittich y Leslie,1988):
Female parent is inoculated in carrot agar and allowed colonize plate by a week.
Is inoculated with a spore suspension from the unknown strain (male). Colony is gently shaked with a glass bar
Are incubated at < 25C under light for 4-6 weeks.
Avoid seal the plate.
If molecular protocols to determine sexual MAT-1and MAT-2 alleles are available, less crosses are required
Positive crosses are definitive. Negative ones are not necessarily conclusive.
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Fusarium teliomorphs morphologic tree (Booth, 1972)
Micronectriella Nectria Calonectria Gibberella
Discolor
Gibbosum
Lateritium
Sporotrichiella
EpisphaeriaArachnites Coccophilum
Artrosporiella
Elegans (F. oxysporum complex)
Albonectria HaematonectriaCyanonectria
Cosmospora
Martiella F. solani complex Liseola G. fujikuroi complexSpicarioides
(From Perez-Vicente and Ploetz, 2014)
Classification in formae speciales by Snyder & Hansen in 1940
W.N. Hansen
W.C. Snyder
1940
Compress the 16 sections in 9 species
> de 150 formae speciales recognized of F. oxysporum
All Elegans section species grouped in a single oxysporum specie
Formae speciales and pathogenic races
Most formae speciales attack a single host specie.
Some of them attack more than one specie: i.e.; F. oxysporum f. sp. cucumerinum attack water melon and cucumber (Cafri et al., 2005).
Genetic bases regarding host specificity are in general unknown (Baayen et al., 2000) even when there is recent findings regarding genes involved in pathogenicity in chromosomes LS (Ma et al., 2010)
It can not be assumed that all individuals in a given single forma special have evolved from a common ancestor. All evidences indicate that monophyletic formae speciales are exceptions (Leslie y Summerell, 2006).
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Palm oil wilt byF. oxysporum f. sp. elaeidis
Fusarium oxysporum diseases in different plant species
F. oxysporum f. sp. lycopersici
Panama disease by F. oxysporum f. sp. cubensis
F. oxysporum f. sp. ciceris
Fusarium oxysporum diseases in different plant species
F. oxysporum f. sp. lentis
F. oxysporum f. sp. cucumeris
F. oxysporum f. sp. melonis
Fusarium oxysporum diseases in different plant species
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F. oxysporum f. sp. asparagi
Fusarium oxysporum f. sp. niveum en melón
F. oxysporum f. sp. cepae
Fusarium oxysporum diseases in different plant species
Fusarium spp. cultures growth rate (in mm after three days) in PDA at 25 y 30°C in complete darkness (Burgess et al., 1994)
Species 25°C 30°CF. acuminatum 25-35 5-28
F. andiyazi 27-33 27-40
F. anthophilum 25-40 20-45
F. armeniacum 44-58 37-54
F. avenaceum 28-40 5-25
F. aywerte 40-45 32-42
F. babinda 25-37 15-22
F. beomiforme 30-39 36-46
F. camptoceras 23-29 20-29
F. chlamydosporum 34-46 37-55
F. compactum 41-54 42-58
F. crookwellense 54-66 15-25
F. culmorum 55-68 15-25
Species 25°C 30°CF. decemcellulare 15-25 11-22
F. dimerum 4-10 5-12
F. equiseti 34-46 28-44
F. graminearum 47-61 5-20
F. heterosporum 28-41 8-30
F. hostae 24-29 20-24
F. konzum 21-34 21-38
F. lateritium 8-20 5-15
F. longipes 37-54 44-61
F. merismoides 4-10 5-12
F. musarum 50-59 44-49
F. napiforme 20-35 20-32
F. nelsonii 24-39 26-41
Fusarium spp. cultures growth rate (in mmafter three days) in PDA at 25 y 30°C incomplete darkness (Burgess et al., 1994)
Species 25°C 30°C
F. decemcellulare 15-25 11-22
F. dimerum 4-10 5-12
F. equiseti 34-46 28-44
F. graminearum 47-61 5-20
F. heterosporum 28-41 8-30
F. hostae 24-29 20-24
F. konzum 21-34 21-38
F. lateritium 8-20 5-15
F. longipes 37-54 44-61
F. merismoides 4-10 5-12
F. musarum 50-59 44-49
F. napiforme 20-35 20-32
F. nelsonii 24-39 26-41
Species 25°C 30°C
F. nurragi 32-40 6-22
F. nygamai 25-35 32-42
F. oxysporum 25-40 25-40
F. poae 42-54 24-39
F. polyphialidicum 23-40 20-38
F. proliferatum 25-35 25-32
F. pseudograminearum 39-51 10-25
F. pseudonygamai 24-30 24-29
F. redolens 32-37 33-39
F. sambucinum 24-35 11-21
F. semitectum 35-45 16-33
F. scirpi 36-48 36-49
F. solani 21-29 26-36
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Species 25°C 30°C
F. sporotrichioides 51-61 32-42
F. subglutinans 23-37 11-34
F. thapsinum 19-28 14-27
F. tricinctum 29-39 2-15
F. verticillioides 21-30 22-35
Fusarium spp. cultures growth rate (in mm after three days) in PDA at 25 y 30°C in complete darkness (Burgess et al., 1994)
Biological concept: F. oxysporum case; vegetative compatibility groups (VCGs).
F. oxysporum is causal agent of an important number of disease with wilt syndrome. The fungus has not known teleomorph.
Are morphologically identical, and have been differentiated by pathogenicity to specific hosts in formae speciales
In some species, races are not genetically defined as in Fusarium oxysporum f. sp. cubense. Vegetative compatibility has allowed to determine population structures.
In other cases has not been so useful.
Further more specific informations on the technique will be provide.
The phylogenetic concept: sequences of genome’s conserved sectors
In Fusarium phylogenetic analysis, genomic sequences of one or several genes in different analysis types have been used :
β-tubulin (tub-2),
The translation elongation factor 1-α (tef-1),
Histone H3
Portions of coding region of nuclear or mitocondrial DNA
– Intergenic spacers (IGS)
– ITS spaces
Different techniques has been used:
RFLP
AFLP
PCR
RAPDs
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The translation elongation factor 1-∞(TEF) gen codify an essential protein of translation machinery with a high phylogenetic utility due to (Geiser et al., 2006):
(i) Is highly informative at Fusarium species level;
(ii) Have not been detected orthologous copies of Fusarium genera.
(iii) Appears as a single copy and its sequence has a high polymorphism in genome of many closely related Fusarium
(iv) Has been designed universal primers that work thorough the width of all phylogenic genera.
(v) These primers (ef1 and ef2) amplify a ~700 bp of TEF region and kept three introns that complete the half of the amplicon length in all Fusarium species.
The phylogenetic concept: sequences of genome’s conserved sectors 1-∞(TEF)
Larger intergenic spacers (IGS) has been very widely used in phylogenetic studies in Fusarium due to:
(i) Appears as the more rapid evolved spacer region in genome
(ii) Is a very conserved region of nuclear rDNA with sufficient polymorphism to may show considerable differences between close related species and subspecies.
(iii) Appears in multicopies in genome
The phylogenetic concept: sequences of genome’s conserved sectors: IGS
Fusarium ID database v. 1.0 (Geiser et al., 2006)
Complex of species Represented species
Gibberella fujikuroi speciescomplex:Excelent representation
Fusarium acutatum, F. andiyazi, F. anthophilum, F. bactridioides, F. begoniae, F. brevicatenulatum, F. bulbicola, F. circinatum, F. circinatum, F. sp. cf. concentricum, F. denticulatum, F. dlaminii, F. fractiflexum, F. fujikuroi, F. globosum, F. guttiforme, F. konzum, F. lactis, F. mangiferae, F. napiforme, F. nygamai, F. phyllophilum, F. proliferatum, F. pseudoanthophilum, F. pseudocircinatum, F. pseudonygamai, F. ramigenum, F. sacchari, F. sterilihyphosum, F. subglutinans, F. succisae, F. thapsinum, F. udum, F. verticillioides y 20 spp.no descritas
Fusarium type A trichoteceneproducer species and relatives: Weak representation
Fusarium cerealis (=F. crookwellense), F. culmorum, F. graminearum y 8 spp. relacionadas; F. lunulosporum, F. pseudograminearum
F. oxysporum and relatives: Good representation.
Fusarium commune, F. hostae, F. miscanthi, 45 linajes decf. ‘F. oxysporum’, F. redolens.
F. solani species complex : Good representation.
Fusarium phaseoli, 25 linajes de cf. ‘F. solani ’, F. tucumaniae, F. virguliforme.
Other linages: Poor representation
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Results influenced by the concept approach
Eg.: Fusarium moniliforme: By decades considered causal agent stalk and ear rot of corn; stem and grain rot of sorghum; bakanae in rice; pokkah boeng in sugarcane.
According the concept: Morphologic: Fusarium moniliforme sensu lato (wide sense) Biologic:
– F. verticillioides: stalk and ear corn rot (produce fumonisin)
– F. tapsinum: stalk and grain sorghum rot (produce few fumonisin and high amounts of moniliformin).
Phylogenetic:
– F. andiyazi (beside F. verticillioides and F. tapsinum), few or any aproduction of fumonisin and moniliformin and not toxic to dugs.
O’Donnell et al. (1998)Sequenced of several genes
Elongation factor 1Microsatelitesmall repeats
Strains of a forma specialis are not necessarily monophyletic
Phylogenetic relationship between VCGs in Foc(RFLP) (Koenig et al., 1997)
Foc VI 0122
Foc V 01214
Foc II 0120
Foc III 01213, 0120, 0121
Foc VII 0123
Foc II 0120, 0126
Foc IV 01210, 0129
Foc IX 01210, 01211
Clados VCGs
Foc I 0124, 0124/0125
Foc VIII 01212 Foc IV 0124, 0125
Foc X 0123
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PCR-RFLP analysis of rRNA IGS region, and digestion of IGS amplicon with enzymes (AvaI, BceAI, BbvI, Csp6I, BsrDI) to differenciate Foc linages (Foure et al., 2009)
8 linages were differentiated:→ I (VCG 01219)→ II (VCGs 1210, 0126)→ III (VCG 01211)→ IV (VCGS 0120, 0122, 01215)→ V (VCGs 0121, 01213)→ VI (VCGs 0124, 0125, 0128, 01220)→ VII (VCGs 0123, 01217, 01218)→ VIII (VCGs (01214)
Specie complex Complex of species
Fusarium taxonomy evolution since the introduction of phylogenetic concept
Fusarium oxysporum f. sp. cubense population grouping according different characterization methods
Method GroupingI II
Actual race classification Race 4 Races 1 and 2. (Stover, 1962 b; Su et al. 1977)
Formación de lacinia en K2 Present (not always) Not present (Sun et al., 1978).
Vegetative compatibility 0120, 0121, 0122, 0126, 0123, 0124, 0125 0128, (Ploetz, 1990 a y b; Brake et al., 0129, 01211, 01213/16, 01210*, 01212, 01214, 1990; Pegg et al., 1993; 01215, 01219 01217, 01218, 01220 Moore et al., 1993).
Volatile production Odoratum inodoratum (not always) (Moore, 1994).
RAPD-PCR RAPD-PCR group 1 RAPD-PCR group 2 (Sorensen, et al. 1993; Sorensen et al., 1994)
Chromosomic number Ek I Ek II genome size. high low(Boehm et al., 1994)
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Flux graphic for Fusarium species identification
Diseased plant
Fusarium isolation(Is necessary to
know more?)No
Answer: Fusarium sp.
Subculture in Carnation leaf Yes
Purification
PDA Carnation leaf agar
SNA
Colony morphology: Rate of growth Pigmentation
Chlamydospore production
Macroconidia:Shape, size
Microconidia:Shape, size, formation
Collect together morphologic, physiologic, hosts, geographic information
Identification process I
Can be identified on base of this information?
F. solani / F. oxysporum
List A of species
Determination of mating groups (MAT)
Sexual crosses
Host rangeVCGsBiologic fertility
Molecular diagnostic
TAXON IDENTIFICATIONTAXON IDENTIFICATION
Identification process II
No. More details are requiredYes
List B of species List C of species
Formae specialis identification
G. fujikuroispecies complex
Molecular diagnostic
Flux graphic for Fusarium species identification
Species more commonly isolated that can be identified by different data types
Species more commonly isolated that can be identified by different data types
Only morphologySPECIES LIST A
Fertility in sexual crosses
SPECIES LIST B
DNA dataSPECIES LIST C
F. acuminatum, F. avenaceum, F. chlamidosporum, F. compactum, F. crookwellense, F. culmorum, F. decemcellulare, F. dimerum, F. equiseti, F. gramianearum, F. longipes, F. merismoides, F. oxysporum, F. poae, F. pseudograminearum, F. scirpi, F. semitectum, F. solani, F. sporotrichoides, F. torulosum,F. tricinctum
F. circinatum, F. fujikuroi,
F. proliferatum, F. sacchari,
F. sambucinum,F. subglutinans,
F. thapsinum,F. verticilloides
Remanent species of Gibberella fujikuroi complex
Many formae specialis of F . oxysporum and F. solani.
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